mmg_233_2013_genetics_genomicswikiaorg-20200214-history
ZFIN
The Zebrafish Model Organism Database (ZFIN) was created in 1994 to consolidate and share research data steming from projects utilizing zebrafish as the model organism. The database contains a wide array of genetic and developmental information, and is one of the leading reference repositories for zebrafish based studies (1). NIH, the funding source for ZFIN, also funds the Zebrafish International Resource Center (ZIRC) which makes available zebrafish lines, probes, and other zebrafish resources (1). ZFIN and ZIRC are complimentary, as ZFIN can be utilized for project design, while ZIRC can be used to obtain the necessary fish and reagents. The sites are integrated, allowing a researcher to find the line of fish needed for a particular experiment on ZFIN and simply follow an embedded link to order the line from ZIRC (specific fish lines or reagents generated in labs other than ZIRC vary with regard to their one click availability). Accessing the Database The homepage (Fig. 1) shows the major components of the site and the links can be navigated to reach the desired destination. The fastest way to look for data related to a particular topic is to do a site search (Fig. 1 - top right). For example, if ZFIN is site searched for the semaphorin receptor Plexin-A1 (plxna1) the database will return all information related to plxna1 displayed by category (Fig. 2). The researcher can then select what aspect of the topic is of interest, plxna1 gene information is a good example (Fig. 2 - lower panel). From this point forward there are a number of avenues the researcher could take from gene sequence and expression to gene ontology. ZFIN Home.png|FIGURE 1. The Zebrafish Model Organism Database homepage. Highlighted in red are the categorical classifications of information in the database and the site search tool (1).|link=http://zfin.org/ Searching the Database.png|FIGURE 2. Inputting a site search will return all related data by category (highlighted in red). Further information can be gained by navigating these categories, gene information is shown in the lower panel as an example (1).|link=http://zfin.org/action/quicksearch/query?query=plxna1 Recent Studies Due to the ease with which zebrafish can be genetically manipulated their use as a model species has been on the increase. ZFIN has a publications section which is routinely updated to highlight new studies and projects. Some examples of recent work done in zebrafish are Characterization and Expression Analysis of mcoln1.1 and mcoln1.2, the Putative Zebrafish Co-orthologs of the Gene Responsible for Human Mucolipidosis type IV (2) and Meta-analysis of toxicity and teratogenicity of 133 chemicals from zebrafish developmental toxicity studies (3). Zebrafish as a Model Organism Zebrafish make an ideal model organism for a number of factors (some of which will be repeated from above). Major development is rapid, coming to completion within 72 hours. For this reason zebrafish are a prime model for developmental studies. Zebrafish are mainly transparent throughout development which allows for visualization of probes, antibodies, and or highlighted structures. Large clutches allow for a relatively low cost and easily replaceable system. Zebrafish are externally fertilized, making embryos readily available for manipulation (1). Lastly, ethical concerns when working with zebrafish are minimal when compared to studies based in mice or rats. ZFIN Wiki The ZFIN database has a Wiki under the community tab. The Wiki is split into two main sections; protocols and antibodies. The protocols section can be searched for a particular method or simply browsed by clicking on the hyper-linked protocols text above the search box. Similarly the antibody section of the Wiki can be accessed via search or through the hyperlink. The antibodies are grouped based upon who submitted the information, and users will often make comments with regard to the efficacy of the antibody. References 1.Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Howe, D.G., Knight, J., Mani, P., Martin, R., Moxon, S.A., Paddock, H., Pich, C., Ramachandran, S., Ruef, B.J., Ruzicka, L., Bauer Schaper, H., Schaper, K., Shao, X., Singer, A., Sprague, J., Sprunger, B., Van Slyke, C., and Westerfield, M. (2011) ZFIN: enhancements and updates to the zebrafish model organism database. Nucleic Acids Res.. 39(suppl 1):D822-D829 2. Benini, A., Bozzato, A., Mantovanelli, S., Calvarini, L., Giacopuzzi, E., Bresciani, R., Moleri, S., Zizioli, D., Beltrame, M., and Borsani, G. (2013) Characterization and expression analysis of mcoln1.1 and mcoln1.2, the putative zebrafish co-orthologs of the gene responsible for human mucolipidosis type IV. Int. J. Dev. Biol. 57(1): 85-93. 3. Ducharme, N.A., Peterson, L.E., Benfenati, E., Reif, D., McCollum, C.W., Gustafsson, J.A., and Bondesson, M. (2013) Meta-analysis of toxicity and teratogenicity of 133 chemicals from zebrafish developmental toxicity studies. Reprod. Toxicol. 41: 98-108. 4. Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF. 1995. Stages of embryonic development of the zebrafish. Developmental Dynamics 203: 253-310